| Year |
Citation |
Score |
| 2020 |
Nguyen Y, Nettleton D. rmRNAseq: Differential Expression Analysis for Repeated-measures RNA-seq Data. Bioinformatics (Oxford, England). PMID 32449749 DOI: 10.1093/Bioinformatics/Btaa525 |
0.311 |
|
| 2019 |
Landau W, Niemi J, Nettleton D. Fully Bayesian analysis of RNA-seq counts for the detection of gene expression heterosis. Journal of the American Statistical Association. 114: 610-621. PMID 31354180 DOI: 10.1080/01621459.2018.1497496 |
0.437 |
|
| 2018 |
Yang J, Yeh CE, Kastoori Ramamurthy R, Qi X, Fernando RL, Dekkers JCM, Garrick DJ, Nettleton D, Schnable PS. Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize. G3 (Bethesda, Md.). PMID 30213868 DOI: 10.1534/G3.118.200636 |
0.318 |
|
| 2018 |
Qi M, Zheng W, Zhao X, Hohenstein JD, Kandel Y, O'Conner S, Wang Y, Du C, Nettleton D, MacIntosh GC, Tylka GL, Wurtele ES, Whitham SA, Li L. QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. Plant Biotechnology Journal. PMID 29878511 DOI: 10.1111/Pbi.12961 |
0.339 |
|
| 2018 |
Liang K, Du C, You H, Nettleton D. A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets. Bmc Bioinformatics. 19: 107. PMID 29587646 DOI: 10.1186/S12859-018-2106-5 |
0.394 |
|
| 2018 |
Baldauf JA, Marcon C, Lithio A, Vedder L, Altrogge L, Piepho HP, Schoof H, Nettleton D, Hochholdinger F. Single-Parent Expression Is a General Mechanism Driving Extensive Complementation of Non-syntenic Genes in Maize Hybrids. Current Biology : Cb. PMID 29358068 DOI: 10.1016/J.Cub.2017.12.027 |
0.459 |
|
| 2018 |
Xu Y, Li Y, Nettleton D. Nested Hierarchical Functional Data Modeling and Inference for the Analysis of Functional Plant Phenotypes Journal of the American Statistical Association. 113: 593-606. DOI: 10.1080/01621459.2017.1366907 |
0.325 |
|
| 2017 |
Kusmec A, Srinivasan S, Nettleton D, Schnable PS. Distinct genetic architectures for phenotype means and plasticities in Zea mays. Nature Plants. 3: 715-723. PMID 29150689 DOI: 10.1038/S41477-017-0007-7 |
0.329 |
|
| 2017 |
Lin HY, Liu Q, Li X, Yang J, Liu S, Huang Y, Scanlon MJ, Nettleton D, Schnable PS. Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS. Genome Biology. 18: 192. PMID 29041960 DOI: 10.1186/S13059-017-1328-6 |
0.402 |
|
| 2017 |
Surana P, Xu R, Fuerst G, Chapman AV, Nettleton D, Wise RP. Inter-chromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen. G3 (Bethesda, Md.). PMID 28790145 DOI: 10.1534/G3.117.300125 |
0.384 |
|
| 2017 |
Hey S, Baldauf J, Opitz N, Lithio A, Pasha A, Provart N, Nettleton D, Hochholdinger F. Complexity and specificity of the maize (Zea mays L.) root hair transcriptome. Journal of Experimental Botany. PMID 28398587 DOI: 10.1093/Jxb/Erx104 |
0.435 |
|
| 2017 |
Tai H, Opitz N, Lithio A, Lu X, Nettleton D, Hochholdinger F. Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.). Journal of Experimental Botany. 68: 403-414. PMID 28204533 DOI: 10.1093/Jxb/Erw422 |
0.459 |
|
| 2017 |
Guan X, Okazaki Y, Lithio A, Li L, Zhao X, Jin H, Nettleton D, Saito K, Nikolau BJ. The 3-hydroxyacyl-ACP dehydratase component of the plant mitochondrial fatty acid synthase system. Plant Physiology. PMID 28202596 DOI: 10.1104/Pp.16.01732 |
0.333 |
|
| 2016 |
Marcon C, Paschold A, Malik WA, Lithio A, Baldauf J, Altrogge L, Opitz N, Lanz C, Schoof H, Nettleton D, Piepho HP, Hochholdinger F. Stability of single parent gene expression complementation in maize hybrids upon water deficit stress. Plant Physiology. PMID 27999083 DOI: 10.1104/Pp.16.01045 |
0.42 |
|
| 2016 |
Jones DC, Zheng W, Huang S, Du C, Zhao X, Yennamalli RM, Sen TZ, Nettleton D, Wurtele ES, Li L. A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence. Frontiers in Plant Science. 7: 983. PMID 27462324 DOI: 10.3389/Fpls.2016.00983 |
0.433 |
|
| 2016 |
Zuo T, Zhang J, Lithio A, Dash S, Weber DF, Wise R, Nettleton D, Peterson T. Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations. Genetics. PMID 27129738 DOI: 10.1534/Genetics.116.188235 |
0.418 |
|
| 2016 |
Yu P, Baldauf J, Lithio A, Marcon C, Nettleton D, Li C, Hochholdinger F. Root type specific reprogramming of maize pericycle transcriptomes by local high nitrate results in disparate lateral root branching patterns. Plant Physiology. PMID 26811190 DOI: 10.1104/Pp.15.01885 |
0.307 |
|
| 2016 |
Liu H, Nguyen YT, Nettleton D, Dekkers JC, Tuggle CK. Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake. Bmc Genomics. 17: 73. PMID 26801403 DOI: 10.1186/S12864-016-2395-X |
0.306 |
|
| 2015 |
Niemi J, Mittman E, Landau W, Nettleton D. Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis. Journal of Agricultural, Biological, and Environmental Statistics. 20: 614-628. PMID 27147815 DOI: 10.1007/S13253-015-0230-5 |
0.425 |
|
| 2015 |
Lithio A, Nettleton D. Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes. Journal of Agricultural, Biological, and Environmental Statistics. 20: 598-613. PMID 27110090 DOI: 10.1007/S13253-015-0232-3 |
0.375 |
|
| 2015 |
Nguyen Y, Nettleton D, Liu H, Tuggle CK. Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates. Journal of Agricultural, Biological, and Environmental Statistics. 20: 577-597. PMID 26660449 DOI: 10.1007/S13253-015-0226-1 |
0.426 |
|
| 2015 |
Tai H, Lu X, Opitz N, Marcon C, Paschold A, Lithio A, Nettleton D, Hochholdinger F. Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.). Journal of Experimental Botany. PMID 26628518 DOI: 10.1093/Jxb/Erv513 |
0.381 |
|
| 2015 |
Li L, Zheng W, Zhu Y, Ye H, Tang B, Arendsee ZW, Jones D, Li R, Ortiz D, Zhao X, Du C, Nettleton D, Scott MP, Salas-Fernandez MG, Yin Y, et al. QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions. Proceedings of the National Academy of Sciences of the United States of America. PMID 26554020 DOI: 10.1073/Pnas.1514670112 |
0.346 |
|
| 2015 |
Opitz N, Marcon C, Paschold A, Malik WA, Lithio A, Brandt R, Piepho HP, Nettleton D, Hochholdinger F. Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit. Journal of Experimental Botany. PMID 26463995 DOI: 10.1093/Jxb/Erv453 |
0.374 |
|
| 2015 |
Yang J, Jiang H, Yeh CT, Yu J, Jeddeloh JA, Nettleton D, Schnable PS. Extreme Phenotype-Genome-Wide Association Study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel. The Plant Journal : For Cell and Molecular Biology. PMID 26386250 DOI: 10.1111/Tpj.13029 |
0.354 |
|
| 2015 |
Jiang F, An C, Bao Y, Zhao X, Jernigan RL, Lithio A, Nettleton D, Li L, Wurtele ES, Nolan LK, Lu C, Li G. ArcA Controls Metabolism, Chemotaxis and Motility Contributing to the Pathogenicity of Avian Pathogenic E. coli. Infection and Immunity. PMID 26099584 DOI: 10.1128/Iai.00312-15 |
0.366 |
|
| 2015 |
Xu W, Meng Y, Surana P, Fuerst G, Nettleton D, Wise RP. The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions. Frontiers in Plant Science. 6: 409. PMID 26089830 DOI: 10.3389/Fpls.2015.00409 |
0.437 |
|
| 2015 |
Whigham E, Qi S, Mistry D, Surana P, Xu R, Fuerst GS, Pliego C, Bindschedler LV, Spanu P, Dickerson JA, Innes R, Nettleton D, Bogdanove AJ, Wise RP. Broadly conserved fungal effector BEC1019 suppresses host cell death and enhances pathogen virulence in powdery mildew of barley (Hordeum vulgare L.). Molecular Plant-Microbe Interactions : Mpmi. PMID 25938194 DOI: 10.1094/Mpmi-02-15-0027-Fi |
0.376 |
|
| 2015 |
Li L, Hill-Skinner S, Liu S, Beuchle D, Tang HM, Yeh CT, Nettleton D, Schnable PS. The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase. The Plant Journal : For Cell and Molecular Biology. 81: 493-504. PMID 25495051 DOI: 10.1111/Tpj.12745 |
0.425 |
|
| 2015 |
Knetter SM, Bearson SM, Huang TH, Kurkiewicz D, Schroyen M, Nettleton D, Berman D, Cohen V, Lunney JK, Ramer-Tait AE, Wannemuehler MJ, Tuggle CK. Salmonella enterica serovar Typhimurium-infected pigs with different shedding levels exhibit distinct clinical, peripheral cytokine and transcriptomic immune response phenotypes. Innate Immunity. 21: 227-41. PMID 24632525 DOI: 10.1177/1753425914525812 |
0.336 |
|
| 2014 |
Ji T, Liu P, Nettleton D. Estimation and Testing of Gene Expression Heterosis. Journal of Agricultural, Biological, and Environmental Statistics. 19: 319-337. PMID 25435758 DOI: 10.1007/S13253-014-0173-2 |
0.46 |
|
| 2014 |
Paschold A, Larson NB, Marcon C, Schnable JC, Yeh CT, Lanz C, Nettleton D, Piepho HP, Schnable PS, Hochholdinger F. Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids. The Plant Cell. 26: 3939-48. PMID 25315323 DOI: 10.1105/Tpc.114.130948 |
0.438 |
|
| 2014 |
Yu X, Lund SP, Greenwald JW, Records AH, Scott RA, Nettleton D, Lindow SE, Gross DC, Beattie GA. Transcriptional analysis of the global regulatory networks active in Pseudomonas syringae during leaf colonization. Mbio. 5: e01683-14. PMID 25182327 DOI: 10.1128/Mbio.01683-14 |
0.381 |
|
| 2014 |
Orr M, Liu P, Nettleton D. An improved method for computing q-values when the distribution of effect sizes is asymmetric. Bioinformatics (Oxford, England). 30: 3044-53. PMID 25024290 DOI: 10.1093/Bioinformatics/Btu432 |
0.407 |
|
| 2014 |
Wang H, Nettleton D, Ying K. Copy number variation detection using next generation sequencing read counts Bmc Bioinformatics. 15. PMID 24731174 DOI: 10.1186/1471-2105-15-109 |
0.305 |
|
| 2014 |
Cernadas RA, Doyle EL, Niño-Liu DO, Wilkins KE, Bancroft T, Wang L, Schmidt CL, Caldo R, Yang B, White FF, Nettleton D, Wise RP, Bogdanove AJ. Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. Plos Pathogens. 10: e1003972. PMID 24586171 DOI: 10.1371/Journal.Ppat.1003972 |
0.401 |
|
| 2014 |
Gu T, Zhu MJ, Schroyen M, Qu L, Nettleton D, Kuhar D, Lunney JK, Ross JW, Zhao SH, Tuggle CK. Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation. Bmc Genomics. 15: 156. PMID 24564230 DOI: 10.1186/1471-2164-15-156 |
0.423 |
|
| 2014 |
Tang HM, Liu S, Hill-Skinner S, Wu W, Reed D, Yeh CT, Nettleton D, Schnable PS. The maize brown midrib2 (bm2) gene encodes a methylenetetrahydrofolate reductase that contributes to lignin accumulation. The Plant Journal : For Cell and Molecular Biology. 77: 380-92. PMID 24286468 DOI: 10.1111/Tpj.12394 |
0.424 |
|
| 2014 |
Wise R, Surana P, Fuerst G, Xu R, Mistry D, Dickerson J, Nettleton D. Flor Revisited (Again): eQTL and Mutational Analysis of NB-LRR Mediated Immunity to Powdery Mildew in Barley Journal of Integrative Agriculture. 13: 237-243. DOI: 10.1016/S2095-3119(13)60651-6 |
0.43 |
|
| 2013 |
Yu X, Lund SP, Scott RA, Greenwald JW, Records AH, Nettleton D, Lindow SE, Gross DC, Beattie GA. Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites. Proceedings of the National Academy of Sciences of the United States of America. 110: E425-34. PMID 23319638 DOI: 10.1073/Pnas.1221892110 |
0.342 |
|
| 2013 |
Aluru M, Zola J, Nettleton D, Aluru S. Reverse engineering and analysis of large genome-scale gene networks. Nucleic Acids Research. 41: e24. PMID 23042249 DOI: 10.1093/Nar/Gks904 |
0.339 |
|
| 2012 |
Lund SP, Nettleton D, McCarthy DJ, Smyth GK. Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Statistical Applications in Genetics and Molecular Biology. 11. PMID 23104842 DOI: 10.1515/1544-6115.1826 |
0.41 |
|
| 2012 |
Paschold A, Jia Y, Marcon C, Lund S, Larson NB, Yeh CT, Ossowski S, Lanz C, Nettleton D, Schnable PS, Hochholdinger F. Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. Genome Research. 22: 2445-54. PMID 23086286 DOI: 10.1101/Gr.138461.112 |
0.416 |
|
| 2012 |
Qu L, Nettleton D, Dekkers JC. A hierarchical semiparametric model for incorporating intergene information for analysis of genomic data. Biometrics. 68: 1168-77. PMID 22994883 DOI: 10.1111/J.1541-0420.2012.01778.X |
0.406 |
|
| 2012 |
Takacs EM, Li J, Du C, Ponnala L, Janick-Buckner D, Yu J, Muehlbauer GJ, Schnable PS, Timmermans MC, Sun Q, Nettleton D, Scanlon MJ. Ontogeny of the maize shoot apical meristem. The Plant Cell. 24: 3219-34. PMID 22911570 DOI: 10.1105/Tpc.112.099614 |
0.334 |
|
| 2012 |
Wilke VL, Nettleton D, Wymore MJ, Gallup JM, Demirkale CY, Ackermann MR, Tuggle CK, Ramer-Tait AE, Wannemuehler MJ, Jergens AE. Gene expression in intestinal mucosal biopsy specimens obtained from dogs with chronic enteropathy. American Journal of Veterinary Research. 73: 1219-29. PMID 22849683 DOI: 10.2460/Ajvr.73.8.1219 |
0.394 |
|
| 2012 |
Liu S, Ying K, Yeh CT, Yang J, Swanson-Wagner R, Wu W, Richmond T, Gerhardt DJ, Lai J, Springer N, Nettleton D, Jeddeloh JA, Schnable PS. Changes in genome content generated via segregation of non-allelic homologs. The Plant Journal : For Cell and Molecular Biology. 72: 390-9. PMID 22731681 DOI: 10.1111/J.1365-313X.2012.05087.X |
0.331 |
|
| 2012 |
Ji T, Liu P, Nettleton D. Borrowing information across genes and experiments for improved error variance estimation in microarray data analysis. Statistical Applications in Genetics and Molecular Biology. 11: Article 12. PMID 22611597 DOI: 10.1515/1544-6115.1806 |
0.392 |
|
| 2012 |
Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS. Gene mapping via bulked segregant RNA-Seq (BSR-Seq). Plos One. 7: e36406. PMID 22586469 DOI: 10.1371/Journal.Pone.0036406 |
0.437 |
|
| 2012 |
Qu L, Nettleton D, Dekkers JC. Improved estimation of the noncentrality parameter distribution from a large number of t-statistics, with applications to false discovery rate estimation in microarray data analysis. Biometrics. 68: 1178-87. PMID 22551000 DOI: 10.1111/J.1541-0420.2012.01764.X |
0.312 |
|
| 2012 |
Hewezi T, Maier TR, Nettleton D, Baum TJ. The Arabidopsis microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection. Plant Physiology. 159: 321-35. PMID 22419826 DOI: 10.1104/Pp.112.193649 |
0.311 |
|
| 2012 |
Lund SP, Nettleton D. The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data Annals of Applied Statistics. 6: 1118-1133. DOI: 10.1214/12-Aoas535 |
0.429 |
|
| 2012 |
Orr M, Liu P, Nettleton D. Estimating the Number of Genes That Are Differentially Expressed in Both of Two Independent Experiments Journal of Agricultural, Biological, and Environmental Statistics. 17: 583-600. DOI: 10.1007/S13253-012-0108-8 |
0.393 |
|
| 2011 |
Huang TH, Uthe JJ, Bearson SM, Demirkale CY, Nettleton D, Knetter S, Christian C, Ramer-Tait AE, Wannemuehler MJ, Tuggle CK. Distinct peripheral blood RNA responses to Salmonella in pigs differing in Salmonella shedding levels: intersection of IFNG, TLR and miRNA pathways. Plos One. 6: e28768. PMID 22174891 DOI: 10.1371/Journal.Pone.0028768 |
0.407 |
|
| 2011 |
Uthe JJ, Qu L, Couture O, Bearson SM, O'Connor AM, McKean JD, Torres YR, Dekkers JC, Nettleton D, Tuggle CK. Use of bioinformatic SNP predictions in differentially expressed genes to find SNPs associated with Salmonella colonization in swine. Journal of Animal Breeding and Genetics = Zeitschrift FüR TierzüChtung Und ZüChtungsbiologie. 128: 354-65. PMID 21906181 DOI: 10.1111/J.1439-0388.2011.00935.X |
0.382 |
|
| 2011 |
Uthe JJ, Bearson SM, Qu L, Dekkers JC, Nettleton D, Rodriguez Torres Y, O'Connor AM, McKean JD, Tuggle CK. Integrating comparative expression profiling data and association of SNPs with Salmonella shedding for improved food safety and porcine disease resistance. Animal Genetics. 42: 521-34. PMID 21906103 DOI: 10.1111/J.1365-2052.2010.02171.X |
0.375 |
|
| 2011 |
Liu JZ, Horstman HD, Braun E, Graham MA, Zhang C, Navarre D, Qiu WL, Lee Y, Nettleton D, Hill JH, Whitham SA. Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development. Plant Physiology. 157: 1363-78. PMID 21878550 DOI: 10.1104/Pp.111.185686 |
0.362 |
|
| 2011 |
Schneider KT, van de Mortel M, Bancroft TJ, Braun E, Nettleton D, Nelson RT, Frederick RD, Baum TJ, Graham MA, Whitham SA. Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation. Plant Physiology. 157: 355-71. PMID 21791600 DOI: 10.1104/Pp.111.181149 |
0.412 |
|
| 2011 |
Kandoth PK, Ithal N, Recknor J, Maier T, Nettleton D, Baum TJ, Mitchum MG. The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells. Plant Physiology. 155: 1960-75. PMID 21335526 DOI: 10.1104/Pp.110.167536 |
0.392 |
|
| 2011 |
Moscou MJ, Lauter N, Caldo RA, Nettleton D, Wise RP. Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions. Molecular Plant-Microbe Interactions : Mpmi. 24: 694-705. PMID 21323465 DOI: 10.1094/Mpmi-09-10-0211 |
0.407 |
|
| 2010 |
Fu Y, Springer NM, Ying K, Yeh CT, Iniguez AL, Richmond T, Wu W, Barbazuk B, Nettleton D, Jeddeloh J, Schnable PS. High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. Plos One. 5: e14178. PMID 21152036 DOI: 10.1371/Journal.Pone.0014178 |
0.312 |
|
| 2010 |
Ciraci C, Tuggle CK, Wannemuehler MJ, Nettleton D, Lamont SJ. Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin. Bmc Genomics. 11: 545. PMID 20929591 DOI: 10.1186/1471-2164-11-545 |
0.362 |
|
| 2010 |
Lkhagvadorj S, Qu L, Cai W, Couture OP, Barb CR, Hausman GJ, Nettleton D, Anderson LL, Dekkers JC, Tuggle CK. Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency. American Journal of Physiology. Regulatory, Integrative and Comparative Physiology. 298: R494-507. PMID 19939971 DOI: 10.1152/Ajpregu.00632.2009 |
0.379 |
|
| 2010 |
Demirkale CY, Nettleton D, Maiti T. Linear mixed model selection for false discovery rate control in microarray data analysis. Biometrics. 66: 621-9. PMID 19522873 DOI: 10.1111/J.1541-0420.2009.01286.X |
0.435 |
|
| 2009 |
Swanson-Wagner RA, DeCook R, Jia Y, Bancroft T, Ji T, Zhao X, Nettleton D, Schnable PS. Paternal dominance of trans-eQTL influences gene expression patterns in maize hybrids. Science (New York, N.Y.). 326: 1118-20. PMID 19965432 DOI: 10.1126/Science.1178294 |
0.448 |
|
| 2009 |
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, ... ... Nettleton D, et al. The B73 maize genome: complexity, diversity, and dynamics. Science (New York, N.Y.). 326: 1112-5. PMID 19965430 DOI: 10.1126/Science.1178534 |
0.376 |
|
| 2009 |
Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. Plos Genetics. 5: e1000734. PMID 19956538 DOI: 10.1371/Journal.Pgen.1000734 |
0.356 |
|
| 2009 |
Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, Schnable PS. Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. Plos Genetics. 5: e1000737. PMID 19936292 DOI: 10.1371/Journal.Pgen.1000737 |
0.384 |
|
| 2009 |
Xi L, Moscou MJ, Meng Y, Xu W, Caldo RA, Shaver M, Nettleton D, Wise RP. Transcript-based cloning of RRP46, a regulator of rRNA processing and R gene-independent cell death in barley-powdery mildew interactions. The Plant Cell. 21: 3280-95. PMID 19861556 DOI: 10.1105/Tpc.109.066167 |
0.416 |
|
| 2009 |
Li X, Wei Y, Nettleton D, Brummer EC. Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa. Bmc Plant Biology. 9: 107. PMID 19678936 DOI: 10.1186/1471-2229-9-107 |
0.38 |
|
| 2009 |
Brooks L, Strable J, Zhang X, Ohtsu K, Zhou R, Sarkar A, Hargreaves S, Elshire RJ, Eudy D, Pawlowska T, Ware D, Janick-Buckner D, Buckner B, Timmermans MCP, Schnable PS, ... Nettleton D, et al. Microdissection of shoot meristem functional domains Plos Genetics. 5. PMID 19424435 DOI: 10.1371/Journal.Pgen.1000476 |
0.422 |
|
| 2009 |
Liu Z, Henderson AL, Nettleton D, Wilson-Welder JH, Hostetter JM, Ramer-Tait A, Jergens AE, Wannemuehler MJ. Mucosal gene expression profiles following the colonization of immunocompetent defined-flora C3H mice with Helicobacter bilis: a prelude to typhlocolitis. Microbes and Infection / Institut Pasteur. 11: 374-83. PMID 19397886 DOI: 10.1016/J.Micinf.2008.12.013 |
0.383 |
|
| 2009 |
Lkhagvadorj S, Qu L, Cai W, Couture OP, Barb CR, Hausman GJ, Nettleton D, Anderson LL, Dekkers JC, Tuggle CK. Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant. Physiological Genomics. 38: 98-111. PMID 19366786 DOI: 10.1152/Physiolgenomics.90372.2008 |
0.406 |
|
| 2009 |
Elling AA, Mitreva M, Gai X, Martin J, Recknor J, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ. Sequence mining and transcript profiling to explore cyst nematode parasitism. Bmc Genomics. 10: 58. PMID 19183474 DOI: 10.1186/1471-2164-10-58 |
0.314 |
|
| 2009 |
Li L, Foster CM, Gan Q, Nettleton D, James MG, Myers AM, Wurtele ES. Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves. The Plant Journal : For Cell and Molecular Biology. 58: 485-98. PMID 19154206 DOI: 10.1111/J.1365-313X.2009.03793.X |
0.386 |
|
| 2009 |
Uthe JJ, Wang Y, Qu L, Nettleton D, Tuggle CK, Bearson SM. Correlating blood immune parameters and a CCT7 genetic variant with the shedding of Salmonella enterica serovar Typhimurium in swine. Veterinary Microbiology. 135: 384-8. PMID 18996651 DOI: 10.1016/J.Vetmic.2008.09.074 |
0.326 |
|
| 2008 |
Skibbe DS, Wang X, Borsuk LA, Ashlock DA, Nettleton D, Schnable PS. Floret-specific differences in gene expression and support for the hypothesis that tapetal degeneration of Zea mays L. occurs via programmed cell death. Journal of Genetics and Genomics = Yi Chuan Xue Bao. 35: 603-16. PMID 18937917 DOI: 10.1016/S1673-8527(08)60081-8 |
0.427 |
|
| 2008 |
Tuggle CK, Wang YF, Couture OP, Qu L, Uthe JJ, Kuhar D, Lunney JK, Nettleton D, Dekkers JC, Bearson SM. Computational integration of structural and functional genomics data across species to develop information on the porcine inflammatory gene regulatory pathway. Developments in Biologicals. 132: 105-13. PMID 18817292 DOI: 10.1159/000317150 |
0.439 |
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| 2008 |
Wang Y, Couture OP, Qu L, Uthe JJ, Bearson SM, Kuhar D, Lunney JK, Nettleton D, Dekkers JC, Tuggle CK. Analysis of porcine transcriptional response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the mesenteric lymph node. Bmc Genomics. 9: 437. PMID 18811943 DOI: 10.1186/1471-2164-9-437 |
0.43 |
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| 2008 |
Strable J, Borsuk L, Nettleton D, Schnable PS, Irish EE. Microarray analysis of vegetative phase change in maize. The Plant Journal : For Cell and Molecular Biology. 56: 1045-57. PMID 18764925 DOI: 10.1111/J.1365-313X.2008.03661.X |
0.345 |
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| 2008 |
Flagel L, Udall J, Nettleton D, Wendel J. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. Bmc Biology. 6: 16. PMID 18416842 DOI: 10.1186/1741-7007-6-16 |
0.378 |
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| 2008 |
Wang D, Nettleton D. Combining classical trait and microarray data to dissect transcriptional regulation: a case study. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 116: 683-90. PMID 18189124 DOI: 10.1007/S00122-007-0701-3 |
0.415 |
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| 2008 |
Guo B, Wang Y, Shi F, Barton YW, Plummer P, Reynolds DL, Nettleton D, Grinnage-Pulley T, Lin J, Zhang Q. CmeR functions as a pleiotropic regulator and is required for optimal colonization of Campylobacter jejuni in vivo. Journal of Bacteriology. 190: 1879-90. PMID 18178742 DOI: 10.1128/Jb.01796-07 |
0.423 |
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| 2008 |
Nettleton D, Recknor J, Reecy JM. Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis. Bioinformatics (Oxford, England). 24: 192-201. PMID 18042553 DOI: 10.1093/Bioinformatics/Btm583 |
0.452 |
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| 2007 |
Elling AA, Mitreva M, Recknor J, Gai X, Martin J, Maier TR, McDermott JP, Hewezi T, McK Bird D, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ. Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. Genome Biology. 8: R211. PMID 17919324 DOI: 10.1186/Gb-2007-8-10-R211 |
0.339 |
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| 2007 |
Madsen ML, Oneal MJ, Gardner SW, Strait EL, Nettleton D, Thacker EL, Minion FC. Array-based genomic comparative hybridization analysis of field strains of Mycoplasma hyopneumoniae. Journal of Bacteriology. 189: 7977-82. PMID 17873054 DOI: 10.1128/Jb.01068-07 |
0.304 |
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| 2007 |
Dembinsky D, Woll K, Saleem M, Liu Y, Fu Y, Borsuk LA, Lamkemeyer T, Fladerer C, Madlung J, Barbazuk B, Nordheim A, Nettleton D, Schnable PS, Hochholdinger F. Transcriptomic and proteomic analyses of pericycle cells of the maize primary root. Plant Physiology. 145: 575-88. PMID 17766395 DOI: 10.1104/Pp.107.106203 |
0.418 |
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| 2007 |
Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MC, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon MJ, Schnable PS. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). The Plant Journal : For Cell and Molecular Biology. 52: 391-404. PMID 17764504 DOI: 10.1111/J.1365-313X.2007.03244.X |
0.459 |
|
| 2007 |
van de Mortel M, Recknor JC, Graham MA, Nettleton D, Dittman JD, Nelson RT, Godoy CV, Abdelnoor RV, Almeida AM, Baum TJ, Whitham SA. Distinct biphasic mRNA changes in response to Asian soybean rust infection. Molecular Plant-Microbe Interactions : Mpmi. 20: 887-99. PMID 17722693 DOI: 10.1094/Mpmi-20-8-0887 |
0.424 |
|
| 2007 |
Ruppert D, Nettleton D, Hwang JT. Exploring the information in p-values for the analysis and planning of multiple-test experiments. Biometrics. 63: 483-95. PMID 17715492 DOI: 10.1111/J.1541-0420.2006.00704.X |
0.304 |
|
| 2007 |
Zhang X, Madi S, Borsuk L, Nettleton D, Elshire RJ, Buckner B, Janick-Buckner D, Beck J, Timmermans M, Schnable PS, Scanlon MJ. Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem. Plos Genetics. 3: e101. PMID 17571927 DOI: 10.1371/Journal.Pgen.0030101 |
0.465 |
|
| 2007 |
Ithal N, Recknor J, Nettleton D, Maier T, Baum TJ, Mitchum MG. Developmental transcript profiling of cyst nematode feeding cells in soybean roots. Molecular Plant-Microbe Interactions : Mpmi. 20: 510-25. PMID 17506329 DOI: 10.1094/Mpmi-20-5-0510 |
0.391 |
|
| 2007 |
Wang Y, Qu L, Uthe JJ, Bearson SM, Kuhar D, Lunney JK, Couture OP, Nettleton D, Dekkers JC, Tuggle CK. Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium. Genomics. 90: 72-84. PMID 17499962 DOI: 10.1016/J.Ygeno.2007.03.018 |
0.405 |
|
| 2007 |
Yang C, Guo R, Jie F, Nettleton D, Peng J, Carr T, Yeakley JM, Fan JB, Whitham SA. Spatial analysis of arabidopsis thaliana gene expression in response to Turnip mosaic virus infection. Molecular Plant-Microbe Interactions : Mpmi. 20: 358-70. PMID 17427806 DOI: 10.1094/Mpmi-20-4-0358 |
0.387 |
|
| 2007 |
Udall JA, Flagel LE, Cheung F, Woodward AW, Hovav R, Rapp RA, Swanson JM, Lee JJ, Gingle AR, Nettleton D, Town CD, Chen ZJ, Wendel JF. Spotted cotton oligonucleotide microarrays for gene expression analysis. Bmc Genomics. 8: 81. PMID 17389046 DOI: 10.1186/1471-2164-8-81 |
0.406 |
|
| 2007 |
Ithal N, Recknor J, Nettleton D, Hearne L, Maier T, Baum TJ, Mitchum MG. Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Molecular Plant-Microbe Interactions : Mpmi. 20: 293-305. PMID 17378432 DOI: 10.1094/Mpmi-20-3-0293 |
0.464 |
|
| 2007 |
Zhang W, Carriquiry A, Nettleton D, Dekkers JC. Pooling mRNA in microarray experiments and its effect on power. Bioinformatics (Oxford, England). 23: 1217-24. PMID 17344238 DOI: 10.1093/Bioinformatics/Btm081 |
0.341 |
|
| 2007 |
Jia H, Nettleton D, Peterson JM, Vazquez-Carrillo G, Jannink JL, Scott MP. Comparison of transcript profiles in wild-type and o2 maize endosperm in different genetic backgrounds Crop Science. 47. DOI: 10.2135/Cropsci2006-0002Tpg |
0.386 |
|
| 2006 |
Caldo RA, Nettleton D, Peng J, Wise RP. Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles. Molecular Plant-Microbe Interactions : Mpmi. 19: 939-47. PMID 16941898 DOI: 10.1094/Mpmi-19-0939 |
0.384 |
|
| 2006 |
Wang D, Nettleton D. Identifying genes associated with a quantitative trait or quantitative trait locus via selective transcriptional profiling. Biometrics. 62: 504-14. PMID 16918915 DOI: 10.1111/J.1541-0420.2005.00491.X |
0.397 |
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| 2006 |
Nettleton D, Wang D. Selective transcriptional profiling for trait-based eQTL mapping Animal Genetics. 37: 13-17. PMID 16886997 DOI: 10.1111/J.1365-2052.2006.01478.X |
0.394 |
|
| 2006 |
Zhao SH, Kuhar D, Lunney JK, Dawson H, Guidry C, Uthe JJ, Bearson SM, Recknor J, Nettleton D, Tuggle CK. Gene expression profiling in Salmonella Choleraesuis-infected porcine lung using a long oligonucleotide microarray. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 17: 777-89. PMID 16845603 DOI: 10.1007/S00335-005-0155-3 |
0.401 |
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| 2006 |
Skibbe DS, Wang X, Zhao X, Borsuk LA, Nettleton D, Schnable PS. Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes. Bioinformatics (Oxford, England). 22: 1863-70. PMID 16731695 DOI: 10.1093/Bioinformatics/Btl270 |
0.35 |
|
| 2006 |
Udall JA, Swanson JM, Nettleton D, Percifield RJ, Wendel JF. A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics. 173: 1823-7. PMID 16702424 DOI: 10.1534/Genetics.106.058271 |
0.446 |
|
| 2006 |
Che P, Lall S, Nettleton D, Howell SH. Gene expression programs during shoot, root, and callus development in Arabidopsis tissue culture. Plant Physiology. 141: 620-37. PMID 16648215 DOI: 10.1104/Pp.106.081240 |
0.407 |
|
| 2006 |
Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, Schnable PS. All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proceedings of the National Academy of Sciences of the United States of America. 103: 6805-10. PMID 16641103 DOI: 10.1073/Pnas.0510430103 |
0.404 |
|
| 2006 |
Madsen ML, Nettleton D, Thacker EL, Minion FC. Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays. Microbiology (Reading, England). 152: 937-44. PMID 16549658 DOI: 10.1099/Mic.0.28674-0 |
0.336 |
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| 2006 |
Madsen ML, Nettleton D, Thacker EL, Edwards R, Minion FC. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infection and Immunity. 74: 160-6. PMID 16368969 DOI: 10.1128/Iai.74.1.160-166.2006 |
0.406 |
|
| 2006 |
DeCook R, Lall S, Nettleton D, Howell SH. Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics. 172: 1155-64. PMID 15956669 DOI: 10.1534/Genetics.105.042275 |
0.466 |
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| 2006 |
DeCook R, Nettleton D, Foster C, Wurtele ES. Identifying differentially expressed genes in unreplicated multiple-treatment microarray timecourse experiments Computational Statistics and Data Analysis. 50: 518-532. DOI: 10.1016/J.Csda.2004.09.004 |
0.452 |
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| 2005 |
Cocciolone SM, Nettleton D, Snook ME, Peterson T. Transformation of maize with the p1 transcription factor directs production of silk maysin, a corn earworm resistance factor, in concordance with a hierarchy of floral organ pigmentation. Plant Biotechnology Journal. 3: 225-35. PMID 17173622 DOI: 10.1111/J.1467-7652.2005.00120.X |
0.35 |
|
| 2005 |
Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK. Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig. Genomics. 86: 618-25. PMID 16216716 DOI: 10.1016/J.Ygeno.2005.08.001 |
0.418 |
|
| 2005 |
Woll K, Borsuk LA, Stransky H, Nettleton D, Schnable PS, Hochholdinger F. Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1. Plant Physiology. 139: 1255-67. PMID 16215225 DOI: 10.1104/Pp.105.067330 |
0.408 |
|
| 2005 |
Lee SH, Zhao SH, Recknor JC, Nettleton D, Orley S, Kang SK, Lee BC, Hwang WS, Tuggle CK. Transcriptional profiling using a novel cDNA array identifies differential gene expression during porcine embryo elongation. Molecular Reproduction and Development. 71: 129-39. PMID 15791594 DOI: 10.1002/Mrd.20291 |
0.453 |
|
| 2005 |
Shen C, Nettleton D, Jiang M, Kim SK, Powell-Coffman JA. Roles of the HIF-1 hypoxia-inducible factor during hypoxia response in Caenorhabditis elegans. The Journal of Biological Chemistry. 280: 20580-8. PMID 15781453 DOI: 10.1074/Jbc.M501894200 |
0.36 |
|
| 2005 |
Shen L, Gong J, Caldo RA, Nettleton D, Cook D, Wise RP, Dickerson JA. BarleyBase--an expression profiling database for plant genomics. Nucleic Acids Research. 33: D614-8. PMID 15608273 DOI: 10.1093/Nar/Gki123 |
0.376 |
|
| 2005 |
Zhang X, Medi S, Borsuk L, Nettleton D, Elshire RJ, Buckner B, Janick-Buckner D, Beck J, Timmermans M, Schnable P, Scanlon MJ. Laser microdissection analyses of maize shoot apical meristems reveal domain-specific patterns of gene expression Plos Genetics. DOI: 10.1371/Journal.Pgen.0030101.Eor |
0.349 |
|
| 2004 |
Lall S, Nettleton D, DeCook R, Che P, Howell SH. Quantitative trait loci associated with adventitious shoot formation in tissue culture and the program of shoot development in Arabidopsis. Genetics. 167: 1883-92. PMID 15342526 DOI: 10.1534/Genetics.103.025213 |
0.381 |
|
| 2004 |
Caldo RA, Nettleton D, Wise RP. Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. The Plant Cell. 16: 2514-28. PMID 15319481 DOI: 10.1105/Tpc.104.023382 |
0.418 |
|
| 2004 |
Manly KF, Nettleton D, Hwang JT. Genomics, prior probability, and statistical tests of multiple hypotheses. Genome Research. 14: 997-1001. PMID 15173107 DOI: 10.1101/Gr.2156804 |
0.306 |
|
| 2003 |
Zhao SH, Nettleton D, Liu W, Fitzsimmons C, Ernst CW, Raney NE, Tuggle CK. Complementary DNA macroarray analyses of differential gene expression in porcine fetal and postnatal muscle. Journal of Animal Science. 81: 2179-88. PMID 12968692 DOI: 10.2527/2003.8192179X |
0.384 |
|
| 2003 |
Puthoff DP, Nettleton D, Rodermel SR, Baum TJ. Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles. The Plant Journal : For Cell and Molecular Biology. 33: 911-21. PMID 12609032 DOI: 10.1046/J.1365-313X.2003.01677.X |
0.449 |
|
| 2002 |
Carson JA, Nettleton D, Reecy JM. Differential gene expression in the rat soleus muscle during early work overload-induced hypertrophy. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 16: 207-9. PMID 11744623 DOI: 10.1096/Fj.01-0544Fje |
0.304 |
|
| 2000 |
Nettleton D, Doerge RW. Accounting for variability in the use of permutation testing to detect quantitative trait loci Biometrics. 56: 52-58. PMID 10783776 DOI: 10.1111/J.0006-341X.2000.00052.X |
0.345 |
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